AMBER Archive (2006)

Subject: Re: AMBER: how to reassign charges

From: David A. Case (case_at_scripps.edu)
Date: Wed Aug 09 2006 - 15:43:07 CDT

On Wed, Aug 09, 2006, Lwin, ThuZar wrote:
>
> In following the tutorial on Thermodynamic integration, I am able
> to reproduce closely to the data in the tutorial. However, I have
> question regarding with making the toluene system neutral.

Just to follow up on David Mobley's comments:

The tutorial just followed the procedure suggested by Shirts et al.:

%A M.R. Shirts
%A J.W. Pitera
%A W.C. Swope
%A V.S. Pande
%T Extremely precise free energy calculations of amino acid side chain
analogs: Comparison of common molecular mechanics force fields for proteins
%J J. Chem. Phys.
%V 119
%P 5740-5761
%D 2003

There is no one "right" way to do this...you probably should devise a similar
scheme for ff03.

>
> In all_amino03.in CB of PHE has charge -0.09872. I changed it to
> -0.183400 since the net charge on toluene was 0.08468. I then redid the
> thermodynamic integration. This time my results are not in agreement
> with the experiment. The charging free energy in vacuum now becomes
> almost twice the value of charging in vacuum as in tutorial, besides it
> is a positive value.

This number by itself is not very interesting, nor is it necessarily wrong
that it depends on what charge model you use. You need to subtract two
comparable sides of a cycle, e.g. subtract the value in water from the value
in vacuum, in order to get any number whose "quality" you could evaluate.
(There is no "experiment" that gives the absolute charging free energy.)

...dac

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